{"entity": "researcher", "timestamp": "2026-08-20T20:37:29.763Z", "family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "affiliations": ["Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA. katy@indiana.edu."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126"}}, "publications": [{"entity": "publication", "iuid": "170a4ecdd5054214b01b05bb3c3251d3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/170a4ecdd5054214b01b05bb3c3251d3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/170a4ecdd5054214b01b05bb3c3251d3"}}, "title": "Enabling global image data sharing in the life sciences.", "authors": [{"family": "Bajcsy", "given": "Peter", "initials": "P", "orcid": "0000-0002-6968-2615", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21af7e4a4bda4c4391682864a018922a.json"}}, {"family": "Bhattiprolu", "given": "Sreenivas", "initials": "S"}, {"family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}}, {"family": "Cimini", "given": "Beth A", "initials": "BA", "orcid": "0000-0001-9640-9318", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cbe15524bb604092be6daf433faa9610.json"}}, {"family": "Collinson", "given": "Lucy", "initials": "L", "orcid": "0000-0003-0260-613X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf7d324482f7440ea46e98de50a61a25.json"}}, {"family": "Ellenberg", "given": "Jan", "initials": "J", "orcid": "0000-0001-5909-701X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/67f7ee86921648c09c58203cc33343c5.json"}}, {"family": "Fiolka", "given": "Reto", "initials": "R", "orcid": "0000-0002-4636-5000", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6d57124e94b34f8baf84480fd16b4ae1.json"}}, {"family": "Giger", "given": "Maryellen", "initials": "M", "orcid": "0000-0001-5482-9728", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e799cca204df420b9d4a8cbdfdd64457.json"}}, {"family": "Goscinski", "given": "Wojtek", "initials": "W"}, {"family": "Hartley", "given": "Matthew", "initials": "M", "orcid": "0000-0001-6178-2884", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/891c0d850b244c209d1852b74d2a532f.json"}}, {"family": "Hotaling", "given": "Nathan", "initials": "N", "orcid": "0000-0001-8423-6464", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/919be1b6ecf34615a2c3e2a05f6c01de.json"}}, {"family": "Taylor", "given": "Adam", "initials": "A", "orcid": "0000-0003-0501-8886", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6415444caf2c46daabfea259cc1d093e.json"}}, {"family": "Keppler", "given": "Antje", "initials": "A", "orcid": "0000-0003-4358-2269", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/034f55795b814833a2382917f5206a27.json"}}], "type": "journal article", "published": "2025-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "22", "issue": "4", "pages": "672-676", "issn-l": "1548-7091"}, "abstract": "Despite the importance of imaging in biological and medical research, a large body of informative and precious image data never sees the light of day. To ensure scientific rigor as well as the reuse of data for scientific discovery, image data need to be made FAIR (findable, accessible, interoperable and reusable). Image data experts are working together globally to agree on common data formats, metadata, ontologies and supporting tools toward image data FAIRification. With this Perspective, we call on public funders to join these efforts to support their national scientists. What researchers most urgently need are openly accessible resources for image data storage that are operated under long-term commitments by their funders. Although existing resources in Australia, Japan and Europe are already collaborating to enable global image data sharing, these efforts will fall short unless more countries invest in operating and federating their own open data resources. This will allow us to harvest the enormous potential of existing image data, preventing substantial loss of unrealized value from past investments in imaging acquisition infrastructure.", "doi": "10.1038/s41592-024-02585-z", "pmid": "40155720", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2083445"}, {"db": "pmc", "key": "PMC12617600"}, {"db": "pii", "key": "10.1038/s41592-024-02585-z"}], "notes": [], "created": "2026-08-20T09:03:23.272Z", "modified": "2026-08-20T09:03:23.746Z"}, {"entity": "publication", "iuid": "bbaee73ea2e045e686298d5b4f24e75e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bbaee73ea2e045e686298d5b4f24e75e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bbaee73ea2e045e686298d5b4f24e75e"}}, "title": "Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms.", "authors": [{"family": "Jain", "given": "Yashvardhan", "initials": "Y", "orcid": "0000-0002-6300-5568", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d39b8dea413a4111a4c1bceba33c46db.json"}}, {"family": "Godwin", "given": "Leah L", "initials": "LL"}, {"family": "Joshi", "given": "Sripad", "initials": "S", "orcid": "0000-0001-7598-1227", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9fa03fecf4ac4be29e4563f53e6a3009.json"}}, {"family": "Mandarapu", "given": "Shriya", "initials": "S", "orcid": "0000-0001-5977-0390", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6886b142028456aacbbc0f8f777e752.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}}], "type": "journal article", "published": "2023-08-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "4656", "issn-l": "2041-1723"}, "abstract": "The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the Hacking the Human Body machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We create a dataset containing 880 histology images with 12,901 segmented structures, engaging 1175 teams from 78 countries in community-driven, open-science development of machine learning models. Tissue variations in the dataset pose a major challenge to the teams which they overcome by using color normalization techniques and combining vision transformers with convolutional models. The best model will be productized in the HuBMAP portal to process tissue image datasets at scale in support of Human Reference Atlas construction.", "doi": "10.1038/s41467-023-40291-0", "pmid": "37537179", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10400613"}, {"db": "pii", "key": "10.1038/s41467-023-40291-0"}], "notes": [], "created": "2026-08-20T08:52:42.654Z", "modified": "2026-08-20T08:52:42.876Z"}, {"entity": "publication", "iuid": "a03d7d7db4af4dc482c16af3f719109f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a03d7d7db4af4dc482c16af3f719109f"}}, "title": "Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.", "authors": [{"family": "Quardokus", "given": "Ellen M", "initials": "EM", "orcid": "0000-0001-7655-4833", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6f0359f5e2f9438aaf591324f1110f64.json"}}, {"family": "Saunders", "given": "Diane C", "initials": "DC", "orcid": "0000-0002-8849-6746", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/764f92d32a0d4f2d8c62e84e320ea4ba.json"}}, {"family": "McDonough", "given": "Elizabeth", "initials": "E", "orcid": "0000-0001-7524-8260", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa249579f8a94bfcadd1431c1e636832.json"}}, {"family": "Hickey", "given": "John W", "initials": "JW", "orcid": "0000-0001-9961-7673", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/674e42e6f0594fd3960adce6260edf93.json"}}, {"family": "Werlein", "given": "Christopher", "initials": "C", "orcid": "0000-0002-7694-4257", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6bc20043daa148b69de69326f6967b10.json"}}, {"family": "Surrette", "given": "Christine", "initials": "C"}, {"family": "Rajbhandari", "given": "Presha", "initials": "P"}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM"}, {"family": "Tian", "given": "Hua", "initials": "H", "orcid": "0000-0002-3598-0219", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cce345ef74b347a7a83076f63c53a23d.json"}}, {"family": "Lowery", "given": "Lisa", "initials": "L"}, {"family": "Neumann", "given": "Elizabeth K", "initials": "EK"}, {"family": "Bj\u00f6rklund", "given": "Frida", "initials": "F"}, {"family": "Neelakantan", "given": "Taruna V", "initials": "TV"}, {"family": "Croteau", "given": "Josh", "initials": "J", "orcid": "0000-0002-8142-0482", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5a325b6e1504a8186376dfcfe054a0d.json"}}, {"family": "Wiblin", "given": "Anne E", "initials": "AE", "orcid": "0000-0002-6087-5701", "researcher": {"href": 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"given": "Werner", "initials": "W", "orcid": "0000-0002-1297-9725", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d69ed7ac3f0046369857b4ae1c55ad4b.json"}}, {"family": "Gehlenborg", "given": "Nils", "initials": "N", "orcid": "0000-0003-0327-8297", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83f7f88927584d80b6b5a5447b20dfdb.json"}}, {"family": "Stockwell", "given": "Brent R", "initials": "BR", "orcid": "0000-0002-3532-3868", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81510049c217404d9363381818ba6446.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}, {"family": "Snyder", "given": "Michael P", "initials": "MP", "orcid": "0000-0003-0784-7987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ce9e294ff3b64f7caa770c883d12514c.json"}}, {"family": "Germain", "given": "Ronald N", "initials": "RN", "orcid": "0000-0003-1495-9143", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9bc6225f3eef4506a319016701a261d8.json"}}, {"family": "Camarillo", "given": "Jeannie M", "initials": "JM"}, {"family": "Kelleher", "given": "Neil L", "initials": "NL", "orcid": "0000-0002-8815-3372", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db299d87427049b8972eabe2d9f453a8.json"}}, {"family": "B\u00f6rner", "given": "Katy", "initials": "K", "orcid": "0000-0002-3321-6137", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b8e7ebf67ae49e3b436a7c1252f7126.json"}}, {"family": "Radtke", "given": "Andrea J", "initials": "AJ", "orcid": "0000-0003-4379-8967", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6c54f64fc7c54f7d9279266878839455.json"}}], "type": "journal article", "published": "2023-08-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "20", "issue": "8", "pages": "1174-1178", "issn-l": "1548-7091"}, "abstract": "Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.", "doi": "10.1038/s41592-023-01846-7", "pmid": "37468619", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10406602"}, {"db": "pii", "key": "10.1038/s41592-023-01846-7"}], "notes": [], "created": "2026-08-20T09:02:53.512Z", "modified": "2026-08-20T09:02:54.263Z"}]}